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The major points of this short section:

1. Trait evolution hypotheses must be • You can build a hierarchical arrangement of evaluated/tested anything – Need a phylogeny • To recover the evolutionary history of 2. Phylogenies are hypotheses! organisms we need a method that is – Mo data mo betta – Empirical 3. Taxonomy should reflect phylogeny! – Objective – Names and ranks are meaningful – Testable

Darwin and Linnaean Classification Phylogenetics • Pre-Darwin Classification all true classification is genealogical; that community • Post-Darwin Classification of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike. – Charles Darwin

Willi Hennig (1913-1976) Phylogeny

• A phylogeny is a hypothesis of ancestor- descendent relationships • Usually shown as a cladogram

(C(P(R(W,H))))

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Phylogeny is genealogy Not a pedigree

• Phylogeny is a genealogy writ large • Pedigrees are reticulate

Interpreting a phylogeny You spin me right round

• Stratford, draw a sample • Tips are ______• Nodes are______• Branches are ______• A clade is ______• Traits are plotted ______

Phylogram END DAY 1

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CHRONOGRAM Phylograms: Quantifying differences

You’re like, in the outgroup Higher organisms? – no way dude

• Organisms are only more ancestral or more derived for a set of characters • Never use “higher” or “lower”

What to do with a phylogeny – opsis case study

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Traits Assumptions of Phylogenetics

• Ancestral versus derived • organisms are related through descent • Apomorphic • lineages split (form sister species) • Plesiomorphic – How does this relate to synapomorphies? • Synapomorphy • changes accumulate through time • Symplesiomorphy – How does this relate to autapomorphies • Homologous verses analogous • Useful traits: • synapomorphies largely outnumber • Not useful: homologies – traits that are shared between • Misleading: organisms are there because of common descent and not just similarity

OK… how do we make a phylogeny?

• Choose taxa • Choose characters – Resolution – Not too fast, not too slow • Determine polarity or select outgroup • Group using synapomorphies • Select method – Parsimony – Maximum likelihood – Bayesian methods • If testing a hypothesis of trait evolution map traits on cladogram

END DAY 2

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To make a phylogenetic tree (review Numbers of trees and example) • Choose characters and taxa Number of taxa / Number of trees (unique topologies) • 5 15 • Group by synapomorphies • 6 105

• 7 945 (2t-3)! Over (2^(t-2) (t-2)!) • 8 10,395 • 10 3 x 10^7 • 20 8 x 10^21 • 50 3 x 10^76

Potential to have multiple most parsimonious trees

Bootstrapping and Jackknifing Resolving multiple parsimonious trees

• Leave it as a polytomy (strict consensus) • Majority rule

Confidence in phylogenetic Taxonomy and Phylogenetics hypotheses • Monophyly • Robust phylogeny • Paraphyly • Congruence • Polyphyly – DNA – RNA – Behavior – Geology – parasites

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